VERSION 1.5.4
-------------
o adjust run-time messages into 3 consistent classes: Info (on
progress), Note and Warning.
o include paths.hsa data, the full list of human pathway ID/names
from KEGG, as to help user specify target pathways when calling
pathview.
o updated korg to included over 80 newly added species, such as
sheep, apple, mandarin orange etc. Pathview can work with 3050
species now.
o adjust the definitions of 7 arguments for pathview function:
discrete, limit,bins, both.dirs, trans.fun, low, mid, high. These
used to be a list of two logical elements with "gene" and "cpd" as
the names. They can be vectors of two or one element(s) now. This
makes pathview easier to use now.
o Vigette has been reformatted: add a Citation section, and some
example on reading user data into R, fix a few typos.
VERSION 1.4.2
-------------
o fixed bug in render.kegg.node function, which generates black
lines in some nodes of multiple sample view.
VERSION 1.3.6
-------------
o ajusted node x coordinate by +0.5 to better fit the color blocks
in 2 layer native kegg views.
VERSION 1.3.4
-------------
o updated bods to included an extra column of id.type, the default
gene ID type.
VERSION 1.2.4
-------------
o updated korg to included over 600 newly added species. Pathview
can work with 2970 species now.
o Make returned values from pathview, keggview.native and
keggview.graph functions invisible.
VERSION 1.2.3
-------------
o Fixed bug in node.map function, which produces 0 values when all
multiple genes in a node are NA's.
VERSION 1.2.2
-------------
o Fixed bug in mol.sum function, which generates "incorrect number of
dimension" or NA's when sum.method="median" etc.
VERSION 1.2.1
-------------
o Fixed bug in "missing red disease gene node labels" in diease
pathways. To avoid interfering with node coloring, set all disease
gene labels to black instead.
VERSION 1.1.7
-------------
o Graphviz view can automatic choose different types of legends,
either on nodes, edges or both depending on the specific pathways.
o Vigette has been reformatted: the "Quick start" section added
VERSION 1.1.6
-------------
o Pathview can plot/integrate/compare multiple states/samples in the
same graph. Several functions and data objects are revised:
including pathview, keggview.native, keggview.graph,
render.kegg.node etc. New section on multiple state data with
working exampleshas been added.
o Vigette has been reformatted: Data integration section splitted
into multiple sub-sections.
VERSION 1.1.5
-------------
o Pathview works with species where default KEGG gene ID is not
Entrez Gene. Several functions and data objects are revised:
including pathview, node.map, sim.mol.data, kegg.species.code,
korg. New section on KEGG species and Gene ID usage with working
exampleshas been added.
VERSION 1.1.3
-------------
o Pathview paper published in Bioinformatics
VERSION 1.0.0
-------------
o Initial release with Bioconductor
o Main function: pathview
o Four functional modules:
-Downloader: download.kegg;
-Parser: node.info, combineKEGGnodes, reaction2edge;
-Mapper: node.map, eg2id, id2eg, cpdkegg2name, cpdname2kegg,
cpd2kegg, cpdidmap, kegg.species.code, mol.sum,
sim.mol.data;
-Viewer: keggview.native, keggview.graph, node.color,
col.key, wordwrap, strfit